23SH | pdb_000023sh

The composite Cryo-EM structure of the tail region of bacteriophage RAN69


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 23SH

This is version 1.1 of the entry. See complete history

Literature

Near-complete cryo-EM structure of the Klebsiella pneumoniae podophage RAN69 reveals tail fiber-spike interface and a divergent pre-ejectosome.

Ruan, Z.Hu, H.Wang, A.Shao, Q.Li, X.Xie, L.Sun, Z.Yu, J.Fang, Q.

(2026) Structure 

  • DOI: https://doi.org/10.1016/j.str.2026.05.010
  • Primary Citation Related Structures: 
    23SF, 23SG, 23SH

  • PubMed Abstract: 

    Carbapenem-resistant Klebsiella pneumoniae is a critical-priority pathogen, underscoring the need for alternatives to antibiotics. Bacteriophages are promising agents, yet high-resolution structures of K. pneumoniae phages are scarce. Here, we report near-complete cryo-electron microscopic reconstructions of the K. pneumoniae podophage RAN69 at 3.0-3.4 Å resolution, enabling atomic models for 12 structural components. Complete in situ structures of the long tail fiber (gp9 trimer) and distal tail spike (gp1 trimer) are resolved, revealing a previously unknown binding interface in which the gp1 N-terminal arm wedges between spike-binding domains of gp9. The pre-ejectosome forms a conserved double-layered assembly (gp10 tetramer over gp11 octamer), tethered to the portal by an octameric gp12 that inserts long helices into the portal barrel, with gp20 reinforcing gp11 interfaces. Divergent folds in gp10 and a lysozyme-like gp11 peripheral domain suggest adaptation to host envelopes. These structures advance our understanding of podophage assembly.


  • Organizational Affiliation
    • School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China.

Macromolecule Content 

  • Total Structure Weight: 526.88 kDa 
  • Atom Count: 36,509 
  • Modeled Residue Count: 4,799 
  • Deposited Residue Count: 4,879 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
tail spike gp1A [auth B],
B [auth J],
C [auth O]
577Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0A1P8VW90 (Klebsiella phage vB_KpnP_KpV74)
Explore A0A1P8VW90 
Go to UniProtKB:  A0A1P8VW90
Entity Groups
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UniProt GroupA0A1P8VW90
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
nozzle gp13D [auth T]793Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0AAE9HHJ8 (Klebsiella phage FK1979)
Explore A0AAE9HHJ8 
Go to UniProtKB:  A0AAE9HHJ8
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UniProt GroupA0AAE9HHJ8
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
tail fiber gp9E [auth r],
H [auth i],
I [auth n]
307Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for D1L2Z4 (Klebsiella phage KP34)
Explore D1L2Z4 
Go to UniProtKB:  D1L2Z4
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UniProt GroupD1L2Z4
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
adaptor gp14F [auth Y],
G [auth d]
186Klebsiella phage RAN69Mutation(s): 0 
EC: 3.2.1.28
UniProt
Find proteins for D1L2Y9 (Klebsiella phage KP34)
Explore D1L2Y9 
Go to UniProtKB:  D1L2Y9
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UniProt GroupD1L2Y9
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
portal gp19J [auth w],
K [auth 0]
531Klebsiella phage RAN69Mutation(s): 0 
UniProt
Find proteins for A0AAE9HFU9 (Klebsiella phage FK1979)
Explore A0AAE9HFU9 
Go to UniProtKB:  A0AAE9HFU9
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UniProt GroupA0AAE9HFU9
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158
RECONSTRUCTIONRELION4.0

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentJCYJ20250604174416022
Other governmentA2402025
National Natural Science Foundation of China (NSFC)China32371285

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release
  • Version 1.1: 2026-07-01
    Changes: Data collection, Database references